The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades

摘要: Many studies of human populations have used the male-specific region Y chromosome (MSY) as a marker, but MSY sequence variants traditionally been subject to ascertainment bias. Also, dating haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems mutation rate choice, and possible long-term saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading phylogenies which branch-lengths are proportional time, allowing times-to-most-recent-common-ancestor (TMRCAs) nodes be estimated directly. Here we describe 3.7 Mb each 448 males at mean coverage 51×, yielding 13,261 high-confidence SNPs, 65.9% previously unreported. The resulting phylogeny covers majority known clades, provides date estimates nodes, constitutes robust evolutionary framework for analyzing history other classes mutation. Different clades within tree show subtle significant differences branch lengths root. We also apply set 23 Y-STRs same samples, SNP- STR-based diversity TMRCA systematically compared. Ongoing purifying selection is suggested by our analysis phylogenetic distribution nonsynonymous 15 single-copy genes.